Contacts of the helix formed by residues 108 - 116 (chain M) in PDB entry 2J28
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 108 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57M VAL* 4.4 20.9 - - + -
58M LYS* 6.0 3.6 - - - +
103M TYR* 5.5 3.4 - - + -
106M ASP 3.2 2.2 + - - -
107M GLY* 1.3 75.8 - - - +
109M PRO* 1.3 68.6 - - - +
111M GLU* 2.9 39.0 - - + +
112M LEU* 3.1 29.7 + - + +
115M GLU* 5.9 0.2 - - - +
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Residues in contact with PRO 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M SER* 6.4 0.2 - - - -
31M PHE* 3.5 39.4 - - + -
103M TYR* 4.5 16.1 - - + -
106M ASP* 3.1 25.7 - - + +
107M GLY 3.0 12.1 - - - +
108M VAL* 1.3 93.8 - - - +
110M GLU* 1.3 68.3 + - + +
111M GLU* 3.8 4.3 - - - +
112M LEU* 3.4 7.8 + - - +
113M ALA* 3.5 10.9 + - - +
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Residues in contact with GLU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M PHE* 3.3 34.6 - - + -
109M PRO* 1.3 82.0 - - + +
111M GLU* 1.3 70.9 + - + +
113M ALA* 3.3 4.4 + - + +
114M ARG* 3.3 17.1 + - + +
126M ILE* 3.1 48.9 - - + +
127M LYS 4.7 0.9 - - - +
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Residues in contact with GLU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M GLY 4.0 2.9 - - - +
108M VAL* 2.9 57.2 - - + +
109M PRO* 3.1 7.5 + - - +
110M GLU* 1.3 83.3 + - + +
112M LEU* 1.3 66.0 + - - +
114M ARG* 2.8 7.7 + - - +
115M GLU* 2.5 35.6 - - - +
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Residues in contact with LEU 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M ALA 4.3 3.4 - - - +
53M MET* 2.8 53.2 - - + +
54M THR* 4.5 2.0 - - - +
55M ARG* 5.8 0.2 - - + -
57M VAL* 4.2 23.1 - - + -
58M LYS 5.8 1.8 - - - +
63M ILE* 5.6 0.7 - - + -
103M TYR* 3.2 29.6 - - + +
108M VAL* 3.1 20.5 + - + +
109M PRO 4.0 1.6 - - - +
111M GLU* 1.3 78.5 - - - +
113M ALA* 1.3 57.6 + - - +
115M GLU* 2.6 38.4 + - + -
116M ALA* 3.1 7.2 + - + +
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Residues in contact with ALA 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M PHE* 4.5 8.5 - - + -
33M LEU* 4.2 35.1 - - + +
53M MET* 5.7 4.3 - - - -
101M VAL* 5.4 1.1 - - + -
103M TYR* 4.5 12.8 + - + -
109M PRO 3.5 9.1 + - - +
110M GLU* 3.3 15.2 + - + +
111M GLU 3.2 1.0 - - - -
112M LEU* 1.3 78.6 - - - +
114M ARG* 1.3 59.1 + - - +
116M ALA* 3.7 4.4 + - - +
117M PHE* 3.4 20.6 + - - +
126M ILE* 5.5 2.0 - - - +
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Residues in contact with ARG 114 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031B G 4.5 13.1 + - - -
2467B C 5.7 0.2 + - - -
110M GLU* 3.3 7.4 + - + +
111M GLU* 2.8 10.0 + - - +
112M LEU 2.8 3.6 + - - -
113M ALA* 1.3 73.5 - - - +
115M GLU* 1.3 69.3 + - - +
116M ALA 2.8 10.2 + - - -
117M PHE* 2.7 51.9 - - + -
126M ILE* 6.1 4.5 - - + -
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Residues in contact with GLU 115 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2467B C 4.3 12.0 + - - -
2468B A 5.0 5.7 - - - +
52M ALA 5.3 0.2 - - - -
55M ARG* 4.5 23.5 + - - -
57M VAL* 6.2 3.8 - - + -
111M GLU* 2.5 47.7 - - - +
112M LEU* 2.6 25.7 + - + +
114M ARG* 1.3 88.4 + - - +
116M ALA* 1.3 56.4 + - - +
119M LEU* 5.5 0.3 - - - +
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Residues in contact with ALA 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2467B C 5.7 0.9 - - - -
49M ALA* 3.9 19.3 - - - +
52M ALA* 3.7 38.1 - - + +
53M MET* 4.1 9.4 - - + +
112M LEU* 3.1 9.9 + - + +
113M ALA 3.7 5.2 - - - +
114M ARG 2.8 2.2 + - - -
115M GLU* 1.3 81.8 - - - +
117M PHE* 1.3 57.0 + - - +
118M LYS 3.6 2.7 - - - +
119M LEU* 3.6 16.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il